Genomic analysis

Independent statistical re-analysis and quality control of public amplicon sequencing data for malaria vector surveillance using the GENOSTAT procedure.

The feature Genomic Analysis (GENOSTAT), which is accessed through Transform > Genomic Analysis, integrates genomics quality control with advanced statistical analysis. This case study demonstrates all GENOSTAT dialog tabs using 161 publicly available FASTQ files from the European Nucleotide Archive (ENA) study PRJEB57331.

The dataset originates from a multiplex amplicon panel targeting insecticide-resistance genes in the invasive malaria vector Anopheles stephensi. The analysis focuses exclusively on the 27 quality control (QC) variables produced by GENOSTAT, illustrating the complete workflow from raw sequencing data to publication-ready statistical output.

GENOSTAT enables genomics laboratories and vector-control programs to ensure that only high-integrity sequencing samples advance to downstream variant-calling workflows.

Data source

This case study uses publicly available sequencing data from the European Nucleotide Archive (ENA) study PRJEB57331.

The dataset consists of 161 Illumina MiSeq sequencing runs and includes a mixture of paired-end and single-end FASTQ files generated using a multiplex amplicon panel targeting insecticide-resistance genes in Anopheles stephensi.